Afromobile,
We currently have an instanciation with more than 2600 portals, that is anticipated on hitting >100k portals within 2 years. We have created extra index's on many SQL tables to accomodate for the different way that dnn can use the data for joins. This seemed to assist lookups that were becoming slower.
I can't speak for the store particularly, however, in general, most of the administration tools come to a crashing halt when you start getting over the 1500 portal mark. Not that it crashes, however, the tools are simply not designed for usability at that level. The Host portals screen we had to entirely re-write, and we developed a custom skin module that uses an ajax / lookup to find portals matching partial names.
I have mentioned elsewhere that we also had Bi4ce write a custom core-mod to handle cross-portal users. Even that interface is starting to become unweildy because it uses a dropdown for the portal selection...
Our biggest concern at the moment is database and file system bloat. I would have to check the exact figures however, I think it's about 8Mb file system per 100 Portals just to created the empty directories (not including any files needed). An we have yet to determine the metrics on the SQL side, all I know is that we had to license a dedicated SQL server because the of cost of running that size of a SQL server a maximumASP was outa site.
hope that helps...